The apex court also pulled up the Centre for filing a similar status report on a probe done by a CBI-led Multi Disciplinary Monitoring Agency (MDMA) into unravelling a larger conspiracy behind the killing of the former prime minister.
A bench of Justices L Nageswara Rao and Deepak Gupta asked the state government to inform the court about the decision taken by it under Article 161 of the Constitution.
The article gives a governor the power to pardon a person who has been proved guilty in court.
The top court was hearing the plea of 46-year-old A G Perarivalan, who has sought suspension of his life sentence in the case till the MDMA's probe is completed.
Senior advocate Gopal Sankaranarayanan, appearing for Perarivalan, said though the state has taken a decision on his mercy petition but his application is pending with the governor.
The MDMA was set up in 1998 on the recommendations of the Justice M C Jain Commission of Inquiry which had probed the conspiracy aspect of Gandhi's assassination.
It is headed by a CBI official and comprises officers from the Intelligence Bureau, the Research and Analysis Wing and the Revenue Intelligence, among other agencies.
The top court told the Centre: "Can you tell us what the difference (is) between the status report filed in April 2018 and November 2019. There is no difference at all." "We have gone through all of your status reports filed in the case," it said.
Additional Solicitor General Pinky Anand, appearing for Centre, said the government has not received any response to the letters rogatory (LR) sent to Sri Lanka and other countries.
The Supreme Court had on January 14, expressed its displeasure over the latest status report filed by the MDMA on its probe.
It said it wanted to know about the progress made in the ongoing investigation in the past two years.
On November 5 last year, the apex court had sought within four weeks a latest status report from the MDMA.
It had said the latest report should also include the status of letters rogatory (LRs).
Perarivalan's counsel had earlier said his role was only limited to procuring nine-volt batteries, which were allegedly used in the improvised explosive device (IED) that had killed Gandhi.
On March 14 last year, the apex court had asked the MDMA to file a status report with regard to a LR sent to Sri Lanka for examining one of the accused, Nixon alias Suren, who is lodged in the Colombo jail.
The top court had dismissed a plea of Perarivalan seeking recall of the May 11, 1999, verdict upholding his conviction.
It had said the material brought on record before it does not inspire confidence to interfere with the verdict in which Perarivalan and three others were initially awarded death sentence, which was later commuted to life term.
The CBI had earlier submitted that Perarivalan had even visited Jaffna in Sri Lanka in the first week of June 1990, besides attending a public meeting along with other conspirators which was addressed by former prime minister V P Singh on May 7, 1991 in Tamil Nadu.
Perarivalan's counsel had submitted that he was just a 19-year-old when the incident took place and had no knowledge of what he was doing and for what purpose the batteries were purchased.
Gandhi was assassinated on the night of May 21, 1991 at Sriperumbudur in Tamil Nadu by a woman suicide bomber, identified as Dhanu, at a poll rally.
Fourteen others, including Dhanu herself, were also killed. Gandhi's assassination was perhaps the first case of suicide bombing which had claimed the life of a high-profile leader.
In its May 1999 order, the top court had upheld the death sentence of four convicts -- Perarivalan, Murugan, Santham and Nalini -- in the assassination case.
In April 2000, the Tamil Nadu governor had commuted the death sentence of Nalini on the basis of the state government's recommendation and an appeal by former Congress president and Rajiv Gandhi's widow Sonia Gandhi.
On February 18, 2014, the top court had commuted the death sentence of Perarivalan to life imprisonment, along with that of two other prisoners - Santhan and Murugan - on grounds of a delay of 11 years in deciding their mercy pleas by the Centre.